Re: [R-sig-phylo] Constraining node values in an OUCH analysis
Hi Daniel, There’s a difference between a method being able to handle fossil data, that is a dataset consisting of a non-ultrametric tree an data for all tips including non contemporaneous ones, and a method allowing you to directly specify trait values at nodes. Most trait evolution methods allow you to do the former (I don’t know for sure but I expect OUCH does). For the latter, which you want to do, there is a function in geiger (described in Slater, Harmon, and Alfaro 2012 Evolution), that allows you to place informative prior probability distributions on node trait values based on the fossil record. But this only allows for fitting simple models and not complex OU scenarios you might want to test. As a hack, I’d suggest adding zero length branches to all nodes in your tree and assigning your reconstructed node values to these. This will produce identical results to specifying node values directly. Zero length branches can be problematic for matrix operations required to compute likelihoods in R and so you might need to explore minimally short branch lengths (10^-5 time units has worked for me in the past). This all should have the same effect as specifying node values, but Aaron will need to confirm that it would work in OUCH. I would question though whether this is a good strategy - you’re assuming your ML estimates of node states , presumably inferred under BM, are robust enough to be fixed for subsequent macroevolutionary analyses. Given how dicey ASRs are, even when you include fossil data, this seems a big stretch. If this is a route you really want to go, perhaps explore using a restricted set of inferred node states - for example only those nodes in the extant taxon tree that are directly ancestral to a fossil taxon, to explore how much this approach influences your results. g Graham Slater Peter Buck Post-Doctoral Fellow Department of Paleobiology National Museum of Natural History The Smithsonian Institution [NHB, MRC 121] P.O. Box 37012 (202) 633-1316 slat...@si.edumailto:slat...@si.edu www.fourdimensionalbiology.comhttp://www.fourdimensionalbiology.com On Jun 4, 2015, at 2:50 PM, Daniel Fulop dfulop@gmail.commailto:dfulop@gmail.com wrote: Isn't at least some of this functionality in mvSLOUCH and/or geiger? ...it's definitely the case that mvSLOUCH can handle missing data at the tips, and I think fossil data can be incorporated in it and geiger as well. At least Slater 2013 has code for incorporating fossils in geiger or modified geiger functions. [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.orgmailto:R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] Constraining node values in an OUCH analysis
Oops - sorry Daniel, yes that should have been addressed to Nathan... Graham Slater Peter Buck Post-Doctoral Fellow Department of Paleobiology National Museum of Natural History The Smithsonian Institution [NHB, MRC 121] P.O. Box 37012 (202) 633-1316 slat...@si.edumailto:slat...@si.edu www.fourdimensionalbiology.comhttp://www.fourdimensionalbiology.com On Jun 4, 2015, at 4:27 PM, Daniel Fulop dfulop@gmail.commailto:dfulop@gmail.com wrote: Thanks, Graham ...but I'm not the OP. I was just shooting off a quick lead without actually checking the specifics in case it was useful. [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] Constraining node values in an OUCH analysis
Thanks, Graham ...but I'm not the OP. I was just shooting off a quick lead without actually checking the specifics in case it was useful. [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] Problem with traitDependentBAMM function
Hi Diego, This error occurs when traitDependentBAMM gets a posterior sample with no rate shift, so that is why �the standard deviation is zero�. Now we fixed this issue in the github version of BAMMtools, https://github.com/macroevolution/bammtools By the way, the manuscript describing this is still in review and it's best viewed as experimental until that manuscript is accepted. Let me know if there is any more problem, Huateng - Huateng Huang huate...@umich.edu Department of Ecology and Evolutionary Biology Museum of Zoology University of Michigan Ann Arbor, MI Begin forwarded message: From: Diego Salazar dsala...@ugr.es Subject: [R-sig-phylo] Problem with traitDependentBAMM function Date: June 4, 2015 8:25:10 AM EDT To: r-sig-phylo@r-project.org Hi all, I am using BAMM and BAMMtools for analyse effect of a continuous trait on evolutionary rates. But I have a problem with traitDependentBAMM function, there is a warning which is repeated a lot of times: 1: In cor(rank(x), rank(y)) : the standard deviation is zero On the other hand in results, $estimate and $p.value are NA. My script is this: test-traitDependentBAMM(eventdata, trait, reps=1000, return.full = T, method = 'spearman',logrates = T, two.tailed = T, traitorder = positive) Where evendata is a bammdata object and trait is a vector with trait values and tips of bammdata. Someone knows what is the problem? Thanks in advanced Diego -- Diego Francisco Salazar Tortosa Phd. student Departamento de Ecolog�a Facultad de Ciencias Universidad de Granada Av. Fuente Nueva s/n 18071 Granada Telefono: +34 958241000 ext 20007 Movil: +34 634851132 email:dsala...@ugr.es dftort...@gmail.com ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ _ Dan Rabosky Assistant Professor Curator of Herpetology Museum of Zoology Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor, MI 48109-1079 USA drabo...@umich.edu http://www-personal.umich.edu/~drabosky http://www.lsa.umich.edu/ummz/ _ Dan Rabosky Assistant Professor Curator of Herpetology Museum of Zoology Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor, MI 48109-1079 USA drabo...@umich.edu http://www-personal.umich.edu/~drabosky http://www.lsa.umich.edu/ummz/ [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] Constraining node values in an OUCH analysis
Hi Nathan, Although it is still possible to impute the missing data prior to the analysis, you can fit multivariate models with missing cases (NA values), using the mvMORPH (development version) from my gitHubhttps://github.com/JClavel/mvMORPH/ Non-ultrametric trees (trees with fossil species) are also allowed and you can compute the root state using the param list. HTH, Julien Short example derived after the code of the help page of mvOU:data2-data# put some missing casesdata2[8,2]-NAdata2[25,1]-NA #then you can fit both data2 or data mvOU(tree, data2) From: slat...@si.edu To: dfulop@gmail.com Date: Thu, 4 Jun 2015 21:22:46 + CC: r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] Constraining node values in an OUCH analysis Hi Daniel, There�s a difference between a method being able to handle fossil data, that is a dataset consisting of a non-ultrametric tree an data for all tips including non contemporaneous ones, and a method allowing you to directly specify trait values at nodes. Most trait evolution methods allow you to do the former (I don�t know for sure but I expect OUCH does). For the latter, which you want to do, there is a function in geiger (described in Slater, Harmon, and Alfaro 2012 Evolution), that allows you to place informative prior probability distributions on node trait values based on the fossil record. But this only allows for fitting simple models and not complex OU scenarios you might want to test. As a hack, I�d suggest adding zero length branches to all nodes in your tree and assigning your reconstructed node values to these. This will produce identical results to specifying node values directly. Zero length branches can be problematic for matrix operations required to compute likelihoods in R and so you might need to explore minimally short branch lengths (10^-5 time units has worked for me in the past). This all should have the same effect as specifying node values, but Aaron will need to confirm that it would work in OUCH. I would question though whether this is a good strategy - you�re assuming your ML estimates of node states , presumably inferred under BM, are robust enough to be fixed for subsequent macroevolutionary analyses. Given how dicey ASRs are, even when you include fossil data, this seems a big stretch. If this is a route you really want to go, perhaps explore using a restricted set of inferred node states - for example only those nodes in the extant taxon tree that are directly ancestral to a fossil taxon, to explore how much this approach influences your results. g Graham Slater Peter Buck Post-Doctoral Fellow Department of Paleobiology National Museum of Natural History The Smithsonian Institution [NHB, MRC 121] P.O. Box 37012 (202) 633-1316 slat...@si.edumailto:slat...@si.edu www.fourdimensionalbiology.comhttp://www.fourdimensionalbiology.com On Jun 4, 2015, at 2:50 PM, Daniel Fulop dfulop@gmail.commailto:dfulop@gmail.com wrote: Isn't at least some of this functionality in mvSLOUCH and/or geiger? ...it's definitely the case that mvSLOUCH can handle missing data at the tips, and I think fossil data can be incorporated in it and geiger as well. At least Slater 2013 has code for incorporating fossils in geiger or modified geiger functions. [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.orgmailto:R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] Constraining node values in an OUCH analysis
Couldn't remember, so went and looked. Turns out that NAs are a problem in
the tips. This isn't necessitated by the structure of the problem, only by
the structure of the package, i.e., because ouchtrees are constructed in
ignorance of where the data are. Unfortunately, it will require
substantial refactoring to get this little bit of extra functionality
As for the original poster's question: no, there is currently no way in
'ouch' to incorporate fossil data (i.e., data at internal nodes).
Does anyone know: has someone else already implemented this for the
Ornstein-Uhlenbeck or Brownian motion processes?
A.
On Thu, Jun 4, 2015 at 1:00 PM, David Bapst dwba...@gmail.com wrote:
While contemplating Nate's question, I wondered, doesn't hansen
currently support NA codings for missing variables for tip taxa?
Unfortunately the donotrun{} example for hansen() using geiger data
isn't currently functioning, so I couldn't test this.
--
Aaron A. King, Ph.D.
Ecology Evolutionary Biology
Mathematics
Center for the Study of Complex Systems
University of Michigan
GPG Public Key: 0x15780975
[[alternative HTML version deleted]]
___
R-sig-phylo mailing list - R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] Constraining node values in an OUCH analysis
Aaron,
While contemplating Nate's question, I wondered, doesn't hansen
currently support NA codings for missing variables for tip taxa?
Unfortunately the donotrun{} example for hansen() using geiger data
isn't currently functioning, so I couldn't test this.
-Dave Bapst
On Thu, Jun 4, 2015 at 10:46 AM, Aaron King kin...@umich.edu wrote:
Interesting question, Nate. Do I understand you to say that you have data
on some variables (and not others) at internal nodes? If so, what happens
when you just add those to the data, with NA to indicate missing values?
Have you tried this?
A.
On Thu, Jun 4, 2015 at 11:10 AM, Nathan Thompson
nathan.thomp...@stonybrook.edu wrote:
Hi all,
I am performing an multivariate analysis in ouch on a group of extant
species. I would ideally like to include information for fossil taxa in the
analysis, however, no single fossil taxon preserves all of the variables of
interest. However, I have performed univariate ancestral state
reconstructions (with fossils) and obtained estimates of the node values.
Is there any way, in a multivariate ouch analysis, to 'constrain' nodes to
certain values based on this a priori knowledge of ancestral states?
I realize the alternative would be to just run separate univariate OU
analyses for each variable (including fossils), but I would like to do this
in a multivariate framework.
Thank you,
Nathan E Thompson
Doctoral Candidate
Dept. of Anatomical Sciences
Stony Brook University
nathan.thomp...@stonybrook.edu
[[alternative HTML version deleted]]
___
R-sig-phylo mailing list - R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at
http://www.mail-archive.com/r-sig-phylo@r-project.org/
--
Aaron A. King, Ph.D.
Ecology Evolutionary Biology
Mathematics
Center for the Study of Complex Systems
University of Michigan
GPG Public Key: 0x15780975
[[alternative HTML version deleted]]
___
R-sig-phylo mailing list - R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
--
David W. Bapst, PhD
Adjunct Asst. Professor, Geology and Geol. Eng.
South Dakota School of Mines and Technology
501 E. St. Joseph
Rapid City, SD 57701
http://webpages.sdsmt.edu/~dbapst/
http://cran.r-project.org/web/packages/paleotree/index.html
___
R-sig-phylo mailing list - R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] Constraining node values in an OUCH analysis
Interesting question, Nate. Do I understand you to say that you have data on some variables (and not others) at internal nodes? If so, what happens when you just add those to the data, with NA to indicate missing values? Have you tried this? A. On Thu, Jun 4, 2015 at 11:10 AM, Nathan Thompson nathan.thomp...@stonybrook.edu wrote: Hi all, I am performing an multivariate analysis in ouch on a group of extant species. I would ideally like to include information for fossil taxa in the analysis, however, no single fossil taxon preserves all of the variables of interest. However, I have performed univariate ancestral state reconstructions (with fossils) and obtained estimates of the node values. Is there any way, in a multivariate ouch analysis, to 'constrain' nodes to certain values based on this a priori knowledge of ancestral states? I realize the alternative would be to just run separate univariate OU analyses for each variable (including fossils), but I would like to do this in a multivariate framework. Thank you, Nathan E Thompson Doctoral Candidate Dept. of Anatomical Sciences Stony Brook University nathan.thomp...@stonybrook.edu [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Aaron A. King, Ph.D. Ecology Evolutionary Biology Mathematics Center for the Study of Complex Systems University of Michigan GPG Public Key: 0x15780975 [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
[R-sig-phylo] Constraining node values in an OUCH analysis
Hi all, I am performing an multivariate analysis in ouch on a group of extant species. I would ideally like to include information for fossil taxa in the analysis, however, no single fossil taxon preserves all of the variables of interest. However, I have performed univariate ancestral state reconstructions (with fossils) and obtained estimates of the node values. Is there any way, in a multivariate ouch analysis, to 'constrain' nodes to certain values based on this a priori knowledge of ancestral states? I realize the alternative would be to just run separate univariate OU analyses for each variable (including fossils), but I would like to do this in a multivariate framework. Thank you, Nathan E Thompson Doctoral Candidate Dept. of Anatomical Sciences Stony Brook University nathan.thomp...@stonybrook.edu [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] A perfect storm: phylogenetic trees, random effects and zero-inflated binomial data
Hi all, thank you for your suggestions! I will delve into the suggested packages and may come back to you when the learning curve becomes too steep :-). thanks again, Diederik On 6/3/2015 5:44 PM, Peter Smits wrote: The alternative to MCMCglmm would be to use stan or bugs for writing your own sampling statement + priors. You'll have more control than with MCMCglmm, but it will have even more of a learning curve. Using stan will also most likely be faster than using any single R package. Cheers, Peter On Wed, Jun 3, 2015 at 10:25 AM, Diederik Strubbe diederik.stru...@uantwerpen.be mailto:diederik.stru...@uantwerpen.be wrote: Dear all, I am struggling with analysing a dataset aimed at explaining invasion success of non-native species. At a country level, I need to relate invasion success (binomial: 0 for failed invasions, 1 for success) to socio-economic variables, taking into account - Phylogenetic relatedness among introduced species: including a phylogenetic tree - Country as a random effect - The fact that data are zero-inflated (most introductions fail). Any suggestions for R packages that can handle a binomial response variable, phylogenetic trees, random effects and zero-inflation? Thanks in advance, Diederik -- Dr.Diederik Strubbe Evolutionary Ecology Group Department of Biology University of Antwerp Middelheimcampus GV310 Groenenborgerlaan 171 2020 Antwerpen, Belgium office: +32 3 265 34 69 tel:%2B32%203%20265%2034%2069 mobile phone: +32 477445568 tel:%2B32%20477445568 skype user name: lakrinn [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org mailto:R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Peter D Smits Grad student Committee on Evolutionary Biology University of Chicago psm...@uchicago.edu mailto:psm...@uchicago.edu http://home.uchicago.edu/~psmits/home.html http://home.uchicago.edu/%7Epsmits/home.html [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
[R-sig-phylo] Phylogenetic PCA
Dear all, I'm wondering if there is a package in R with which I can run a phylogenetic PCA. Please, if you know something or if you you know another software useful to use this technique, let me know. Thanks in advance. Best regards, Sérgio. -- Com os melhores cumprimentos, Sérgio Ferreira Cardoso. Best regards, Sérgio Ferreira Cardoso MSc. Paleontology candidate Departamento de Ciências da Terra - FCT /Universidade Nova de Lisboa Geociências - Universidade de Évora Lisboa, Portugal [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] Phylogenetic PCA
Hello Dne Čt 4. června 2015 11:26:10, Sergio Ferreira Cardoso napsal(a): Dear all, I'm wondering if there is a package in R with which I can run a phylogenetic PCA. Please, if you know something or if you you know another software useful to use this technique, let me know. Function ppca from package adephylo. Thanks in advance. Best regards, Sérgio. Regards, Vojtěch -- Vojtěch Zeisek http://trapa.cz/en/ Department of Botany, Faculty of Science Charles University in Prague Benátská 2, Prague, 12801, CZ http://botany.natur.cuni.cz/en/ Institute of Botany, Academy of Science Zámek 1, Průhonice, 25243, CZ http://www.ibot.cas.cz/en/ Czech Republic signature.asc Description: This is a digitally signed message part. ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] Phylogenetic PCA
Hi Sergio, there you go http://blog.phytools.org/2011/04/new-function-phylpca.html http://cran.r-project.org/web/packages/phytools/index.html best wishes 2015-06-04 11:26 GMT+01:00 Sergio Ferreira Cardoso sff.card...@campus.fct.unl.pt: Dear all, I'm wondering if there is a package in R with which I can run a phylogenetic PCA. Please, if you know something or if you you know another software useful to use this technique, let me know. Thanks in advance. Best regards, Sérgio. -- Com os melhores cumprimentos, Sérgio Ferreira Cardoso. Best regards, Sérgio Ferreira Cardoso MSc. Paleontology candidate Departamento de Ciências da Terra - FCT /Universidade Nova de Lisboa Geociências - Universidade de Évora Lisboa, Portugal [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Thomas Püschel PhD student in Adaptive Organismal Biology Computational and Evolutionary Biology Group Faculty of Life Sciences University of Manchester Michael Smith Building Oxford Road Manchester M13 9PT United Kingdom Email: thomas.pusc...@postgrad.manchester.ac.uk thomas.puschelroul...@postgrad.manchester.ac.uk; thomaspusc...@gmail.com [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] Converting species cladogram to dendrogram for heatmap with R
Hi Anand. Have you tried eliminating spaces line breaks from your Newick string. When I do that I am able to read the tree with read.newick with no problem. All the best, Liam Liam J. Revell, Assistant Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://blog.phytools.org On 6/4/2015 1:02 AM, Anand K S Rao wrote: (Mt3.5v5, Mt4.0v1), Car), (((Pvu186, Pvu218), (Gma109, Gma189)), Cca))), (((Ppe139, Mdo196), Fve226), Csa122)), Ath167, Aly107), Cru183), (Bra197, Tha173)), Cpa113), (Gra221, Tca233)), (Csi154, (Ccl165, Ccl182))), ((Mes147, Rco119),(Lus200, (Ptr156, Ptr210, Egr201)), Vvi145), ((Stu206, Sly225), Mgu140)), Aco195), (((Sbi79, Zma181),(Sit164, Pvi202)), (Osa193, Bdi192))), Smo91), Ppa152), (((Cre169, Vca199), Csu227), ((Mpu228, Mpu229), Olu231))); ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
[R-sig-phylo] Problem with traitDependentBAMM function
Hi all, I am using BAMM and BAMMtools for analyse effect of a continuous trait on evolutionary rates. But I have a problem with traitDependentBAMM function, there is a warning which is repeated a lot of times: 1: In cor(rank(x), rank(y)) : the standard deviation is zero On the other hand in results, $estimate and $p.value are NA. My script is this: test-traitDependentBAMM(eventdata, trait, reps=1000, return.full = T, method = 'spearman',logrates = T, two.tailed = T, traitorder = positive) Where evendata is a bammdata object and trait is a vector with trait values and tips of bammdata. Someone knows what is the problem? Thanks in advanced Diego -- Diego Francisco Salazar Tortosa Phd. student Departamento de Ecología Facultad de Ciencias Universidad de Granada Av. Fuente Nueva s/n 18071 Granada Telefono: +34 958241000 ext 20007 Movil: +34 634851132 email:dsala...@ugr.es dftort...@gmail.com ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] Constraining node values in an OUCH analysis
Isn't at least some of this functionality in mvSLOUCH and/or geiger? ...it's definitely the case that mvSLOUCH can handle missing data at the tips, and I think fossil data can be incorporated in it and geiger as well. At least Slater 2013 has code for incorporating fossils in geiger or modified geiger functions. [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
